Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr8
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 56894857
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1173888 characters in sequence are not A, C, G, or T
File 19 of 185
Found at i:5146379 original size:24 final size:24
Alignment explanation
Indices: 5146351--5146396 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
5146341 ATCATTTTTT
* *
5146351 GCTGCTCATTCATTTGCTTTTGAA
1 GCTGCTCATGCATTTCCTTTTGAA
*
5146375 GCTGCTCCTGCATTTCCTTTTG
1 GCTGCTCATGCATTTCCTTTTG
5146397 GGATTGTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.17, T:0.46
Consensus pattern (24 bp):
GCTGCTCATGCATTTCCTTTTGAA
Found at i:5148693 original size:18 final size:18
Alignment explanation
Indices: 5148672--5148706 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5148662 ATTAATAAAA
5148672 ATAAATAAATAAATATGC
1 ATAAATAAATAAATATGC
* *
5148690 ATAATTATATAAATATG
1 ATAAATAAATAAATATG
5148707 AGAAAAATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.34
Consensus pattern (18 bp):
ATAAATAAATAAATATGC
Found at i:5148871 original size:3 final size:3
Alignment explanation
Indices: 5148865--5148912 Score: 78
Period size: 3 Copynumber: 15.7 Consensus size: 3
5148855 TTACAATACC
*
5148865 AAT AAT AAT ACT AAAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5148911 AA
1 AA
5148913 GGAGAAAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 40 0.95
4 2 0.05
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5151831 original size:25 final size:25
Alignment explanation
Indices: 5151794--5151885 Score: 80
Period size: 25 Copynumber: 3.7 Consensus size: 25
5151784 GAGGATTTTA
*
5151794 TTTTAGTTT-ATATTAATACAATTAT
1 TTTTA-TTTAATATTAATATAATTAT
* *
5151819 TTTTATTTAATATTAATATAA-AAC
1 TTTTATTTAATATTAATATAATTAT
* *
5151843 TTTTATTTAATTTTTATAATAATTAT
1 TTTTATTTAATATTAAT-ATAATTAT
* * *
5151869 TTGTAATTAATTTTAAT
1 TTTTATTTAATATTAAT
5151886 TTATACTTAA
Statistics
Matches: 54, Mismatches: 10, Indels: 5
0.78 0.14 0.07
Matches are distributed among these distances:
24 19 0.35
25 20 0.37
26 15 0.28
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (25 bp):
TTTTATTTAATATTAATATAATTAT
Found at i:5161040 original size:16 final size:17
Alignment explanation
Indices: 5161012--5161043 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
5161002 CATATTATTT
5161012 ATTAAATTAATTTTCTA
1 ATTAAATTAATTTTCTA
5161029 ATTAAA-TAATTTTCT
1 ATTAAATTAATTTTCT
5161044 CAACCCAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTAAATTAATTTTCTA
Found at i:5164735 original size:17 final size:17
Alignment explanation
Indices: 5164698--5164740 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
5164688 TATATATATC
*
5164698 AATATTAAATTAAATAT
1 AATATTAAATTAAATAA
* *
5164715 AATATTAAATTCATTAA
1 AATATTAAATTAAATAA
*
5164732 AATAATAAA
1 AATATTAAA
5164741 ATATTTGGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (17 bp):
AATATTAAATTAAATAA
Found at i:5167421 original size:45 final size:46
Alignment explanation
Indices: 5167354--5167477 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
5167344 CATATGACCT
*
5167354 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCT-AGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCA
*
5167397 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTAAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCA
*
5167443 CTTATCACTTTATCACTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
5167478 CACTTATCAC
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 8 0.11
44 4 0.05
45 21 0.28
46 41 0.55
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (46 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCA
Found at i:5167481 original size:37 final size:37
Alignment explanation
Indices: 5167439--5167652 Score: 392
Period size: 37 Copynumber: 5.8 Consensus size: 37
5167429 AGCTAAAGCT
* **
5167439 ACCACTTATCACTTTATCACTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
*
5167476 GCCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
5167513 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
5167550 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
5167587 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
5167624 ACCACTTATCACTTTGTTTCTTGATCAGA
1 ACCACTTATCACTTTGTTTCTTGATCAGA
5167653 AGTACTCAAA
Statistics
Matches: 172, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 172 1.00
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (37 bp):
ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
Found at i:5170227 original size:26 final size:26
Alignment explanation
Indices: 5170178--5170227 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
5170168 TAAATCAAAT
* **
5170178 ATATATTATAAAATTTTATAAAAACA
1 ATATATTATAAAAATACATAAAAACA
*
5170204 ATATATTATAAAAATACATGAAAA
1 ATATATTATAAAAATACATAAAAA
5170228 TTTTTAAGAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (26 bp):
ATATATTATAAAAATACATAAAAACA
Found at i:5184205 original size:33 final size:28
Alignment explanation
Indices: 5184168--5184235 Score: 73
Period size: 33 Copynumber: 2.2 Consensus size: 28
5184158 GTAAATGAAT
5184168 AAAGAAACAAACAAACAAAACGAAACAGAAATG
1 AAAGAAACAAA-AAA-AAAACGAAA-A-AAA-G
* *
5184201 AAAGAAAGAAAAAAAAAAGGAAAAAAAG
1 AAAGAAACAAAAAAAAAACGAAAAAAAG
5184229 AAAGAAA
1 AAAGAAA
5184236 GGAGAAAGAC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
28 8 0.24
29 3 0.09
30 1 0.03
31 8 0.24
32 3 0.09
33 10 0.30
ACGTcount: A:0.76, C:0.07, G:0.15, T:0.01
Consensus pattern (28 bp):
AAAGAAACAAAAAAAAAACGAAAAAAAG
Found at i:5184235 original size:12 final size:12
Alignment explanation
Indices: 5184201--5184235 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
5184191 AACAGAAATG
5184201 AAAGAAAGAAAA
1 AAAGAAAGAAAA
5184213 AAA-AAAGGAAAA
1 AAAGAAA-GAAAA
5184225 AAAGAAAGAAA
1 AAAGAAAGAAA
5184236 GGAGAAAGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 3 0.14
12 15 0.71
13 3 0.14
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAGAAAGAAAA
Found at i:5185458 original size:16 final size:16
Alignment explanation
Indices: 5185422--5185474 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
5185412 GTTATATACT
* *
5185422 CATGAATTGAGTATGG
1 CATGAAATGAGTATTG
*
5185438 TATGAAATGATGTATT-
1 CATGAAATGA-GTATTG
*
5185454 CATGAATTGAGTATTG
1 CATGAAATGAGTATTG
5185470 CATGA
1 CATGA
5185475 CTGATGTCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 5 0.17
16 21 0.70
17 4 0.13
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.36
Consensus pattern (16 bp):
CATGAAATGAGTATTG
Found at i:5187636 original size:16 final size:16
Alignment explanation
Indices: 5187617--5187651 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
5187607 TTACCAATAC
*
5187617 AATGGATTAGAGGTGT
1 AATGGAATAGAGGTGT
5187633 AATGGAATAGAGGTGT
1 AATGGAATAGAGGTGT
5187649 AAT
1 AAT
5187652 AGCAAATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.34, T:0.29
Consensus pattern (16 bp):
AATGGAATAGAGGTGT
Found at i:5187902 original size:16 final size:16
Alignment explanation
Indices: 5187865--5187906 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
5187855 TTAATCATAT
*
5187865 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
5187881 TT-AAATATATTATAA
1 TTAAAATATATTATAA
5187896 TTAAAATATAT
1 TTAAAATATAT
5187907 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:5187913 original size:14 final size:15
Alignment explanation
Indices: 5187874--5187915 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
5187864 TTTAAACATA
*
5187874 ATTATTATTAAATAT
1 ATTATAATTAAATAT
5187889 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
5187903 A-TATAATTTAATA
1 ATTATAATTAAATA
5187916 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:5204389 original size:21 final size:20
Alignment explanation
Indices: 5204365--5204410 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 20
5204355 AATAAAAAAG
5204365 TTTATATTATTTTGGTATT-TT
1 TTTATATT-TTTT-GTATTATT
5204386 TTTAT-TTTTTTGTATTATT
1 TTTATATTTTTTGTATTATT
5204405 TTTATA
1 TTTATA
5204411 AAAACCCAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 5 0.22
19 11 0.48
20 2 0.09
21 5 0.22
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.74
Consensus pattern (20 bp):
TTTATATTTTTTGTATTATT
Found at i:5204737 original size:26 final size:26
Alignment explanation
Indices: 5204684--5204737 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
5204674 AATATAGAAT
* **
5204684 AATTTATAAATCTAAAATTACATTAA
1 AATTTATAAATCTAAAATTAAAAAAA
5204710 AATTTATAAA-CTAAAATCTAAAAAAA
1 AATTTATAAATCTAAAAT-TAAAAAAA
5204736 AA
1 AA
5204738 CCTTAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.31
Consensus pattern (26 bp):
AATTTATAAATCTAAAATTAAAAAAA
Found at i:5206938 original size:73 final size:71
Alignment explanation
Indices: 5206793--5206940 Score: 158
Period size: 73 Copynumber: 2.1 Consensus size: 71
5206783 AAATATTGGA
* ***
5206793 GGGGCTACTATATTTTTAGGAGGGCTATAATATATATACAAAGGGAGAAATTGCAAAAATTTTAA
1 GGGGCTACTATATTTTTAGGAGGGCCATAATATATATACAAAGGGAGAAATTGCAAAAAAAATAA
5206858 ACCTTG
66 ACCTTG
* * *
5206864 GGGGCCTACTTATATTTTTGGGAGGGCCATAGTATA-ATTACAAA-GGACTAAATTG-AAAAAAA
1 GGGG-CTAC-TATATTTTTAGGAGGGCCATAATATATA-TACAAAGGGA-GAAATTGCAAAAAAA
*
5206926 ATAAACTTTTG
62 ATAAAC-CTTG
5206937 GGGG
1 GGGG
5206941 GCATGGCCCC
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
71 4 0.06
72 18 0.28
73 42 0.66
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (71 bp):
GGGGCTACTATATTTTTAGGAGGGCCATAATATATATACAAAGGGAGAAATTGCAAAAAAAATAA
ACCTTG
Found at i:5207758 original size:86 final size:87
Alignment explanation
Indices: 5207626--5207814 Score: 242
Period size: 86 Copynumber: 2.2 Consensus size: 87
5207616 ACTTAAAAAA
* * * *
5207626 AAAAAGAAACAATTAAGCCCCTACTTTTTTTCCACTCATTTGGGTACTTGAACTTTTAAAATGCA
1 AAAAA-AAGCAATTAAGCCCCTACTTTTTTTCCACTCAATTCGGTACTTGAACTTTCAAAATGCA
5207691 T-AAAAA-AACCTTCAAA-TCTT-
65 TCAAAAAGAACC-TCAAACTCTTC
* *
5207711 AAAAAATGCAATTAAGCCCCTACTTTTTTTTTGCACTCAATTCGGTACTTGAACTTTCAAAATGC
1 AAAAAAAGCAATTAAGCCCCTAC--TTTTTTTCCACTCAATTCGGTACTTGAACTTTCAAAATGC
* *
5207776 ATCAAAAAGATCCTCAAACTTTTC
64 ATCAAAAAGAACCTCAAACTCTTC
5207800 AAAAAAAGCAATTAA
1 AAAAAAAGCAATTAA
5207815 CTCCATGCTT
Statistics
Matches: 89, Mismatches: 9, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
84 16 0.18
85 5 0.06
86 38 0.43
87 10 0.11
88 6 0.07
89 14 0.16
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (87 bp):
AAAAAAAGCAATTAAGCCCCTACTTTTTTTCCACTCAATTCGGTACTTGAACTTTCAAAATGCAT
CAAAAAGAACCTCAAACTCTTC
Found at i:5207899 original size:29 final size:28
Alignment explanation
Indices: 5207866--5207929 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 28
5207856 AATTAAAAAC
*
5207866 AATAAAAG-ATAT-AAATATTATTAAATTTT
1 AATAAAAGAAT-TCAAATATTA--AAAATTT
5207895 AATAAAAGAATTCAAATATTAAAAATTT
1 AATAAAAGAATTCAAATATTAAAAATTT
5207923 AATAAAA
1 AATAAAA
5207930 TTAGAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
28 13 0.41
29 9 0.28
30 10 0.31
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (28 bp):
AATAAAAGAATTCAAATATTAAAAATTT
Found at i:5208002 original size:19 final size:18
Alignment explanation
Indices: 5207941--5208003 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 18
5207931 TAGAAAAAAG
5207941 TAAAATCGTAAAAAATATA
1 TAAAATCGTAAAAAAT-TA
* * **
5207960 AAAAATTGTAAAATTTTA
1 TAAAATCGTAAAAAATTA
5207978 TAAAAATCGTAAAAAAATTA
1 T-AAAATCGT-AAAAAATTA
5207998 TAAAAT
1 TAAAAT
5208004 ATATAGAAAT
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
18 2 0.06
19 24 0.71
20 8 0.24
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (18 bp):
TAAAATCGTAAAAAATTA
Found at i:5208306 original size:36 final size:36
Alignment explanation
Indices: 5208240--5208318 Score: 88
Period size: 35 Copynumber: 2.2 Consensus size: 36
5208230 TCATTAAAAT
* * **
5208240 TTTTTATGATTTTTATAAAATTTTACAATTTTT-TA
1 TTTTTACGAATTTTATAAAAAATTACAATTTTTATA
*
5208275 TTTTTACGAATTTTATAAAAAAATTATAATTTTTAATA
1 TTTTTACGAATTTTAT-AAAAAATTACAATTTTT-ATA
5208313 TTTTTA
1 TTTTTA
5208319 AATTTTTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
35 14 0.39
36 14 0.39
38 8 0.22
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (36 bp):
TTTTTACGAATTTTATAAAAAATTACAATTTTTATA
Found at i:5208332 original size:45 final size:44
Alignment explanation
Indices: 5208257--5208371 Score: 110
Period size: 45 Copynumber: 2.6 Consensus size: 44
5208247 GATTTTTATA
* * *
5208257 AAATTTTACAATTTTTTA-TTTTTACGAATTTTATAAAAAAATT-AT
1 AAATTTTATACTTTTTAATTTTTTA--AATTTTAT-AAAAAATTAAT
* * *
5208302 AATTTTTAATA-TTTTTAAATTTTTTAAATTTTATTAAAATTTAAT
1 AAATTTT-ATACTTTTT-AATTTTTTAAATTTTATAAAAAATTAAT
5208347 AAATTTTATACTTTTTAATTTTTTA
1 AAATTTTATACTTTTTAATTTTTTA
5208372 TATATATTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
44 18 0.31
45 32 0.54
46 3 0.05
47 6 0.10
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (44 bp):
AAATTTTATACTTTTTAATTTTTTAAATTTTATAAAAAATTAAT
Found at i:5208354 original size:10 final size:10
Alignment explanation
Indices: 5208316--5208355 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
5208306 TTTAATATTT
5208316 TTAAATTTT-
1 TTAAATTTTA
5208325 TTAAATTTTA
1 TTAAATTTTA
*
5208335 TTAAAATTTA
1 TTAAATTTTA
*
5208345 ATAAATTTTA
1 TTAAATTTTA
5208355 T
1 T
5208356 ACTTTTTAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
9 9 0.35
10 17 0.65
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
TTAAATTTTA
Found at i:5208520 original size:90 final size:91
Alignment explanation
Indices: 5208404--5208575 Score: 256
Period size: 90 Copynumber: 1.9 Consensus size: 91
5208394 AGAGTAGGGG
* * *
5208404 CTTAATTGCTGTTTTAAAAAATTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAA
1 CTTAATTGCTGTTTTAAAAAAGTTTGAGGGTCTTTTTGATACATTTTGAAAGCTCAAGTACCCAA
5208469 TTGAGTG-AAAAAAAATAAGTAAGGA
66 TTGAGTGCAAAAAAAATAAGTAAGGA
* * * * * *
5208494 CTTAATTGCTTTTTTTAATAAGTTTGAGGGTCTTTTTGATACATTTTGAAAGCTCAGGTGCTCAA
1 CTTAATTGCTGTTTTAAAAAAGTTTGAGGGTCTTTTTGATACATTTTGAAAGCTCAAGTACCCAA
5208559 TTGAGTGCAAAAAAAAT
66 TTGAGTGCAAAAAAAAT
5208576 TAGGAGGGGC
Statistics
Matches: 72, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
90 63 0.88
91 9 0.12
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.38
Consensus pattern (91 bp):
CTTAATTGCTGTTTTAAAAAAGTTTGAGGGTCTTTTTGATACATTTTGAAAGCTCAAGTACCCAA
TTGAGTGCAAAAAAAATAAGTAAGGA
Found at i:5208598 original size:90 final size:89
Alignment explanation
Indices: 5208399--5208622 Score: 252
Period size: 90 Copynumber: 2.5 Consensus size: 89
5208389 TAGTAAGAGT
* * * *
5208399 AGGGGCTTAATTGCTGTTTTAAAAAATTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTA
1 AGGGGCTTAATTGCT-TTTTTAAAAAGTTTGAGGGTCTTTTTGATACATTTTGAAAGCTCAAGTA
*
5208464 CCCAATTGAGTGAAAAAAAATAAGT
65 CCCAATTGAGTGAAAAAAAATAAGG
* * * * *
5208489 AAGGACTTAATTGCTTTTTTTAATAAGTTTGAGGGTCTTTTTGATACATTTTGAAAGCTCAGGTG
1 AGGGGCTTAATTGC-TTTTTTAAAAAGTTTGAGGGTCTTTTTGATACATTTTGAAAGCTCAAGTA
* *
5208554 CTCAATTGAGTGCAAAAAAAATTAGG
65 CCCAATTGAGTG-AAAAAAAATAAGG
* * *
5208580 AGGGGCTTAGTTACTTTTTTTTTAAAACGTTTGAGGGT-TTTTT
1 AGGGGCTTAATTGC---TTTTTTAAAAAGTTTGAGGGTCTTTTT
5208623 ACACCCTTAA
Statistics
Matches: 112, Mismatches: 18, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
90 65 0.58
91 22 0.20
92 5 0.04
93 20 0.18
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.39
Consensus pattern (89 bp):
AGGGGCTTAATTGCTTTTTTAAAAAGTTTGAGGGTCTTTTTGATACATTTTGAAAGCTCAAGTAC
CCAATTGAGTGAAAAAAAATAAGG
Found at i:5217453 original size:29 final size:32
Alignment explanation
Indices: 5217402--5217461 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 32
5217392 AATTTTGTGC
*
5217402 AGGAATACAATTTGGGGCTAAATAGAAGAAAA
1 AGGAATACAATTTGGGGCCAAATAGAAGAAAA
*
5217434 AGGAA-ACAA-TT-GGGCCAAATTGAAGAAA
1 AGGAATACAATTTGGGGCCAAATAGAAGAAA
5217462 GAAGCAAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 15 0.58
30 2 0.08
31 4 0.15
32 5 0.19
ACGTcount: A:0.50, C:0.08, G:0.25, T:0.17
Consensus pattern (32 bp):
AGGAATACAATTTGGGGCCAAATAGAAGAAAA
Found at i:5234778 original size:44 final size:45
Alignment explanation
Indices: 5234687--5234779 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 45
5234677 GTCGCTGTAT
*
5234687 TGGAATAGAGGCGTAATAGCAAGTCAATTGTTTGGTTGAATGTAA
1 TGGAATAGAGGCGTAATAGCAAGTCAATTGTTTGGTTGAATGGAA
* * *
5234732 TGGAATAGAGGCGTAATAG-TATTC-TTGTGTTTGGTTGAATGGAA
1 TGGAATAGAGGCGTAATAGCAAGTCAAT-TGTTTGGTTGAATGGAA
5234776 TGGA
1 TGGA
5234780 GGTGTAATAG
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
43 1 0.02
44 23 0.53
45 19 0.44
ACGTcount: A:0.30, C:0.05, G:0.31, T:0.33
Consensus pattern (45 bp):
TGGAATAGAGGCGTAATAGCAAGTCAATTGTTTGGTTGAATGGAA
Found at i:5234957 original size:18 final size:17
Alignment explanation
Indices: 5234936--5234970 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5234926 TTATTATTAA
*
5234936 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
5234954 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
5234971 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:5235077 original size:18 final size:17
Alignment explanation
Indices: 5235054--5235090 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
5235044 AATTATTATT
5235054 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
5235070 AAATATATGATTTAATA
1 AAATATATGATTTAATA
5235087 AAAT
1 AAAT
5235091 TCTTAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:5235129 original size:120 final size:119
Alignment explanation
Indices: 5234916--5235166 Score: 457
Period size: 120 Copynumber: 2.1 Consensus size: 119
5234906 TTAATCATAT
5234916 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTTAA-ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
*
5234981 CAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAA
65 CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
*
5235036 TTTAAGATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAAT
1 TTTAA-ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
5235101 CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
65 CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
5235156 TTTGAAATAAT
1 TTT-AAATAAT
5235167 ACCTTCAATT
Statistics
Matches: 127, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
120 125 0.98
121 2 0.02
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (119 bp):
TTTAAATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATC
AATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
Found at i:5235149 original size:61 final size:61
Alignment explanation
Indices: 5234964--5235151 Score: 197
Period size: 61 Copynumber: 3.1 Consensus size: 61
5234954 ATATAATTTA
*
5234964 ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
1 ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
* * * * * * * ** * * *
5235025 ATAAAA-T-ATAAT-TTAAGATAATTATTAT-TAAATATATTTTAATTAAAATATATGAT-TT
1 ATAAAATTCTTAATAATCA-AT-ATTCTTATATGAATTTACTAAAATCATAATATATGATACT
5235083 AATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
1 -ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
5235145 ATAAAAT
1 ATAAAAT
5235152 ATAATTTGAA
Statistics
Matches: 95, Mismatches: 24, Indels: 16
0.70 0.18 0.12
Matches are distributed among these distances:
58 3 0.03
59 33 0.35
60 16 0.17
61 40 0.42
62 3 0.03
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.42
Consensus pattern (61 bp):
ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
Found at i:5238261 original size:21 final size:22
Alignment explanation
Indices: 5238216--5238260 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
5238206 AAAAAATTTT
5238216 AATATTAATATCAAGTTTAAAA
1 AATATTAATATCAAGTTTAAAA
*
5238238 AATATTATTATCAAGTTTAAAA
1 AATATTAATATCAAGTTTAAAA
5238260 A
1 A
5238261 TTAACGTTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.38
Consensus pattern (22 bp):
AATATTAATATCAAGTTTAAAA
Found at i:5238676 original size:23 final size:24
Alignment explanation
Indices: 5238616--5238678 Score: 78
Period size: 23 Copynumber: 2.7 Consensus size: 24
5238606 TCTACTCACT
5238616 AACAAATCAAGAACAATTTCCAGC
1 AACAAATCAAGAACAATTTCCAGC
* *
5238640 AGAC-TATCAA-AACAATTTCC-GG
1 A-ACAAATCAAGAACAATTTCCAGC
5238662 AACAAATCAAGAACAAT
1 AACAAATCAAGAACAAT
5238679 ATCAAAACAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
21 2 0.06
22 7 0.21
23 16 0.48
24 6 0.18
25 2 0.06
ACGTcount: A:0.51, C:0.22, G:0.10, T:0.17
Consensus pattern (24 bp):
AACAAATCAAGAACAATTTCCAGC
Found at i:5238710 original size:107 final size:107
Alignment explanation
Indices: 5238588--5238817 Score: 442
Period size: 107 Copynumber: 2.1 Consensus size: 107
5238578 ACTATACTTG
5238588 CAATTTCCAGTTTCATCTTCTACTCACTAACAAATCAAGAACAATTTCCAGCAGACTATCAAAAC
1 CAATTTCCAGTTTCATCTTCTACTCACTAACAAATCAAGAACAATTTCCAGCAGACTATCAAAAC
* *
5238653 AATTTCCGGAACAAATCAAGAACAATATCAAAACAAATGCTA
66 AATTTCCAGAACAAATCAAGAACAATATCAAAACAAATGCAA
5238695 CAATTTCCAGTTTCATCTTCTACTCACTAACAAATCAAGAACAATTTCCAGCAGACTATCAAAAC
1 CAATTTCCAGTTTCATCTTCTACTCACTAACAAATCAAGAACAATTTCCAGCAGACTATCAAAAC
5238760 AATTTCCAGAACAAATCAAGAACAATATCAAAACAAATGCAA
66 AATTTCCAGAACAAATCAAGAACAATATCAAAACAAATGCAA
5238802 CAATTTCCAGTTTCAT
1 CAATTTCCAGTTTCAT
5238818 TGAAAACAGC
Statistics
Matches: 121, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
107 121 1.00
ACGTcount: A:0.43, C:0.24, G:0.07, T:0.25
Consensus pattern (107 bp):
CAATTTCCAGTTTCATCTTCTACTCACTAACAAATCAAGAACAATTTCCAGCAGACTATCAAAAC
AATTTCCAGAACAAATCAAGAACAATATCAAAACAAATGCAA
Found at i:5238783 original size:23 final size:24
Alignment explanation
Indices: 5238723--5238785 Score: 87
Period size: 23 Copynumber: 2.7 Consensus size: 24
5238713 TCTACTCACT
5238723 AACAAATCAAGAACAATTTCCAGC
1 AACAAATCAAGAACAATTTCCAGC
*
5238747 AGAC-TATCAA-AACAATTTCCAG-
1 A-ACAAATCAAGAACAATTTCCAGC
5238769 AACAAATCAAGAACAAT
1 AACAAATCAAGAACAAT
5238786 ATCAAAACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
21 2 0.06
22 6 0.18
23 18 0.53
24 6 0.18
25 2 0.06
ACGTcount: A:0.52, C:0.22, G:0.08, T:0.17
Consensus pattern (24 bp):
AACAAATCAAGAACAATTTCCAGC
Found at i:5238794 original size:22 final size:22
Alignment explanation
Indices: 5238752--5238797 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
5238742 CCAGCAGACT
* *
5238752 ATCAAAACAATTTCCAGAACAA
1 ATCAAAACAATATCCAAAACAA
5238774 ATCAAGAACAATAT-CAAAACAA
1 ATCAA-AACAATATCCAAAACAA
5238796 AT
1 AT
5238798 GCAACAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.59, C:0.20, G:0.04, T:0.17
Consensus pattern (22 bp):
ATCAAAACAATATCCAAAACAA
Found at i:5240132 original size:21 final size:22
Alignment explanation
Indices: 5240090--5240132 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
5240080 AAGTGAACAG
5240090 TGCAATAATCGATGAAGAAGAACC
1 TGCAATAATCGAT--AGAAGAACC
5240114 TGCAATAATCGAT-GAAGAA
1 TGCAATAATCGATAGAAGAA
5240133 AAGGAAGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
24 13 0.68
ACGTcount: A:0.47, C:0.14, G:0.21, T:0.19
Consensus pattern (22 bp):
TGCAATAATCGATAGAAGAACC
Found at i:5246089 original size:22 final size:22
Alignment explanation
Indices: 5246064--5246116 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
5246054 TCTTTCCTTG
* **
5246064 AAAATATCACCATTATAATAAT
1 AAAATATCACAACAATAATAAT
*
5246086 AAAATATCATAACAATAATAAT
1 AAAATATCACAACAATAATAAT
5246108 AAAATATCA
1 AAAATATCA
5246117 AATAAAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.28
Consensus pattern (22 bp):
AAAATATCACAACAATAATAAT
Found at i:5248759 original size:73 final size:68
Alignment explanation
Indices: 5248677--5248815 Score: 179
Period size: 68 Copynumber: 2.0 Consensus size: 68
5248667 TAATTAAACT
** *
5248677 TAATCACTTTAATATTAAATTTAATCTAATATTTATCTACAAGATAAACATTAAATTTAATTTAA
1 TAATCACTTTAATATTAAA-TTAATAAAATA-CTAT-T--AAGATAAACATTAAATTTAATTTAA
5248742 TATTAAGA
61 TATTAAGA
* **
5248750 TAATCACTTTAATATTAGATTAATAAAATACTATTAAGATAAGTATTAAATTTAATTTAATATTA
1 TAATCACTTTAATATTAAATTAATAAAATACTATTAAGATAAACATTAAATTTAATTTAATATTA
5248815 A
66 A
5248816 ATCTATTAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
68 29 0.48
70 1 0.02
71 3 0.05
72 9 0.15
73 18 0.30
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.42
Consensus pattern (68 bp):
TAATCACTTTAATATTAAATTAATAAAATACTATTAAGATAAACATTAAATTTAATTTAATATTA
AGA
Found at i:5263590 original size:5 final size:5
Alignment explanation
Indices: 5263582--5263610 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
5263572 TTAAATTAGG
5263582 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
5263611 CAAAACAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:5273323 original size:55 final size:55
Alignment explanation
Indices: 5273239--5273352 Score: 183
Period size: 55 Copynumber: 2.1 Consensus size: 55
5273229 TACAGCTAAT
*
5273239 TTACGATCACGACTGTCATTTTTAAAGCTCACTGATTTACGATCACAACTTATTC
1 TTACGATCACGACTGTCATTTTTAAAGCTCACTGATTTACAATCACAACTTATTC
* ** *
5273294 TTACGATCACGATTGTCATTTTTAAAGCTCGTTGATTTACAATCACGACTTATTC
1 TTACGATCACGACTGTCATTTTTAAAGCTCACTGATTTACAATCACAACTTATTC
5273349 TTAC
1 TTAC
5273353 AGTTCACTGA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (55 bp):
TTACGATCACGACTGTCATTTTTAAAGCTCACTGATTTACAATCACAACTTATTC
Found at i:5273492 original size:109 final size:109
Alignment explanation
Indices: 5273359--5273942 Score: 647
Period size: 109 Copynumber: 5.4 Consensus size: 109
5273349 TTACAGTTCA
* * * * * *
5273359 CTGATTTCCAATCACGATTGTCATTTTTAAAGCTTGTTGATTTACGATCATGGCTTATTCTTACG
1 CTGATTTACGATCACGACTGTCATTTTTAAAGCTCGTTGATTTACAATCACGGCTTATTCTTACG
* * * * * *
5273424 ATCCACTAATTTATTATCACAACCTTCGGTTTTCTAACAGTTCA
66 ATCCGCTGATTTATAATCACAACCTTCGATTTTCTAACAATTCG
* * * * *
5273468 TTAATTTACGATCACGACTATCATTTTTAAAGCTCGTTGATTTACAATCATGGCTTATTCTTACA
1 CTGATTTACGATCACGACTGTCATTTTTAAAGCTCGTTGATTTACAATCACGGCTTATTCTTACG
* * * * *
5273533 ATACGCTAATTTACAATCACAACCTTCGATTTTCTAACAGTTTG
66 ATCCGCTGATTTATAATCACAACCTTCGATTTTCTAACAATTCG
* * *
5273577 CTGATTTACAATCACAACTGTCATTTTTAAAGCTCGTTGATTTACAATCACGACTTATTCTTACG
1 CTGATTTACGATCACGACTGTCATTTTTAAAGCTCGTTGATTTACAATCACGGCTTATTCTTACG
* * * * * *
5273642 GTCTGCTGATTTATGATCACGACCTTTGGTTTTCTAACAATTCG
66 ATCCGCTGATTTATAATCACAACCTTCGATTTTCTAACAATTCG
* * * * * *
5273686 TTGATTTACGATCACGATTGTCATTTTTAAAGCTTGCTGATTTACGATCACGGTTTATTCTTACG
1 CTGATTTACGATCACGACTGTCATTTTTAAAGCTCGTTGATTTACAATCACGGCTTATTCTTACG
* * * * * **
5273751 ATTCGTTGATTTACAATCACAATCTTCGATTTTCTAGCAATTTT
66 ATCCGCTGATTTATAATCACAACCTTCGATTTTCTAACAATTCG
* ** * *
5273795 CTGAGTTACGATCACGACTGTCATTTTTAAAGCTCGTTGATTTATTATCACAGTTTATTCTT---
1 CTGATTTACGATCACGACTGTCATTTTTAAAGCTCGTTGATTTACAATCACGGCTTATTCTTACG
* * *
5273857 A-CCGTTGATTT-TCAATCACGACCTTCGATTTTCTAACAATTTG
66 ATCCGCTGATTTAT-AATCACAACCTTCGATTTTCTAACAATTCG
*
5273900 CTAATTTACGATCACGACTGTCATTTTTAAAGCTCGTTGATTT
1 CTGATTTACGATCACGACTGTCATTTTTAAAGCTCGTTGATTT
5273943 CTTCAACAAG
Statistics
Matches: 401, Mismatches: 73, Indels: 6
0.84 0.15 0.01
Matches are distributed among these distances:
105 76 0.19
106 1 0.00
109 324 0.81
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (109 bp):
CTGATTTACGATCACGACTGTCATTTTTAAAGCTCGTTGATTTACAATCACGGCTTATTCTTACG
ATCCGCTGATTTATAATCACAACCTTCGATTTTCTAACAATTCG
Found at i:5273661 original size:70 final size:70
Alignment explanation
Indices: 5273294--5273838 Score: 241
Period size: 70 Copynumber: 7.6 Consensus size: 70
5273284 CAACTTATTC
* *
5273294 TTACGATCACGATTGTCATTTTTAAAGCTCGTTGATTTACAATCACGACTTATTCTTACAGT-TC
1 TTACAATCACGACTGTCATTTTTAAAGCTCGTTGATTTACAATCACGACTTATTCTTACAGTCT-
*
5273358 ACTGAT
65 GCTGAT
* * * * * * *
5273364 TTCCAATCACGATTGTCATTTTTAAAGCTTGTTGATTTACGATCATGGCTTATTCTTAC-GATCC
1 TTACAATCACGACTGTCATTTTTAAAGCTCGTTGATTTACAATCACGACTTATTCTTACAG-TCT
* *
5273428 ACTAAT
65 GCTGAT
** * * * * * * * *
5273434 TTATTATCACAACCT-TCGGTTTTCTAACAGTTCATTAATTTACGATCACGACTATCATTTTTAA
1 TTACAATCACGA-CTGTC-ATTTT-TAA-AGCTCGTTGATTTACAATCACGACT-T-ATTCTTAC
*
5273498 AG-CTCGTTGAT
60 AGTCT-GCTGAT
* * * * * * *
5273509 TTACAATCATGGCT-T-ATTCTTACAA--TACGCTAATTTACAATCACAACCTTCGATTTTCTAA
1 TTACAATCACGACTGTCATTTTTA-AAGCT-CGTTGATTTACAATCACGA-CTT--A--TTCTTA
*
5273570 CAGTTTGCTGAT
59 CAGTCTGCTGAT
* *
5273582 TTACAATCACAACTGTCATTTTTAAAGCTCGTTGATTTACAATCACGACTTATTCTTACGGTCTG
1 TTACAATCACGACTGTCATTTTTAAAGCTCGTTGATTTACAATCACGACTTATTCTTACAGTCTG
5273647 CTGAT
66 CTGAT
** * ** ** * * * *
5273652 TTATGATCACGACCTTTGGTTTTCTAACAATTCGTTGATTTACGATCACGATTGTCATTTTTAAA
1 TTACAATCACGA-CTGTCATTTT-TAA-AGCTCGTTGATTTACAATCACGACT-T-ATTCTTACA
5273717 G-CTTGCTGAT
61 GTC-TGCTGAT
* * * * * * * *
5273727 TTACGATCACG-GT-TTATTCTT-ACGATTCGTTGATTTACAATCACAATCTTCGATTTTCTAGC
1 TTACAATCACGACTGTCATTTTTAAAG-CTCGTTGATTTACAATCACGA-CTT--ATTCT-TA-C
* * * *
5273789 AATTTTCTGAG
60 AGTCTGCTGAT
*
5273800 TTACGATCACGACTGTCATTTTTAAAGCTCGTTGATTTA
1 TTACAATCACGACTGTCATTTTTAAAGCTCGTTGATTTA
5273839 TTATCACAGT
Statistics
Matches: 352, Mismatches: 87, Indels: 67
0.70 0.17 0.13
Matches are distributed among these distances:
69 2 0.01
70 130 0.37
71 25 0.07
72 17 0.05
73 80 0.23
74 15 0.04
75 79 0.22
76 4 0.01
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.41
Consensus pattern (70 bp):
TTACAATCACGACTGTCATTTTTAAAGCTCGTTGATTTACAATCACGACTTATTCTTACAGTCTG
CTGAT
Found at i:5273732 original size:36 final size:35
Alignment explanation
Indices: 5273294--5273942 Score: 141
Period size: 36 Copynumber: 18.1 Consensus size: 35
5273284 CAACTTATTC
* * *
5273294 TTACGATCACGATTGTCATTTTTAAAGCTCGTTGAT
1 TTACGATCACGACT-TCATTTTTAAAGCTTGCTGAT
* * * *
5273330 TTACAATCACGACTT-ATTCTTACAG-TTCACTGAT
1 TTACGATCACGACTTCATTTTTAAAGCTT-GCTGAT
* * * *
5273364 TTCCAATCACGATTGTCATTTTTAAAGCTTGTTGAT
1 TTACGATCACGACT-TCATTTTTAAAGCTTGCTGAT
* * * * * ** *
5273400 TTACGATCATGGCTT-ATTCTT-ACGATCCACTAAT
1 TTACGATCACGACTTCATTTTTAAAGCT-TGCTGAT
** * * *
5273434 TTATTATCACAACCTTCGGTTTTCTAACAG-TT-CATTAAT
1 TTACGATCACGA-CTTC-ATTTT-TAA-AGCTTGC--TGAT
* *
5273473 TTACGATCACGACTATCATTTTTAAAGCTCGTTGAT
1 TTACGATCACGACT-TCATTTTTAAAGCTTGCTGAT
* * * * * *
5273509 TTACAATCATGGCTT-ATTCTTACAA--TACGCTAAT
1 TTACGATCACGACTTCATTTTTA-AAGCT-TGCTGAT
* * *
5273543 TTACAATCACAACCTTCGATTTTCTAACAGTTTGCTGAT
1 TTACGATCACGA-CTTC-ATTTT-TAA-AGCTTGCTGAT
* * * *
5273582 TTACAATCACAACTGTCATTTTTAAAGCTCGTTGAT
1 TTACGATCACGACT-TCATTTTTAAAGCTTGCTGAT
* * * *
5273618 TTACAATCACGACTT-ATTCTT-ACGGTCTGCTGAT
1 TTACGATCACGACTTCATTTTTAAAGCT-TGCTGAT
* ** * *
5273652 TTATGATCACGACCTTTGGTTTTCTAACA-ATTCGTTGAT
1 TTACGATCACGA-C-TTCATTTT-TAA-AGCTT-GCTGAT
*
5273691 TTACGATCACGATTGTCATTTTTAAAGCTTGCTGAT
1 TTACGATCACGACT-TCATTTTTAAAGCTTGCTGAT
* * * * * *
5273727 TTACGATCACG-GTTTATTCTT-ACGATTCGTTGAT
1 TTACGATCACGACTTCATTTTTAAAGCTT-GCTGAT
* * * * *
5273761 TTACAATCACAATCTTCGATTTTCTAGCAA-TTTTCTGAG
1 TTACGATCACGA-CTTC-ATTTT-TA--AAGCTTGCTGAT
* *
5273800 TTACGATCACGACTGTCATTTTTAAAGCTCGTTGAT
1 TTACGATCACGACT-TCATTTTTAAAGCTTGCTGAT
** * * * * *
5273836 TTATTATCAC-AGTTTATTCTT--A-C-CGTTGAT
1 TTACGATCACGACTTCATTTTTAAAGCTTGCTGAT
* * ** *
5273866 TTTCAATCACGACCTTCGATTTTCTAACAATTTGCTAAT
1 TTACGATCACGA-CTTC-ATTTT-TAA-AGCTTGCTGAT
* *
5273905 TTACGATCACGACTGTCATTTTTAAAGCTCGTTGAT
1 TTACGATCACGACT-TCATTTTTAAAGCTTGCTGAT
5273941 TT
1 TT
5273943 CTTCAACAAG
Statistics
Matches: 437, Mismatches: 120, Indels: 112
0.65 0.18 0.17
Matches are distributed among these distances:
30 14 0.03
31 2 0.00
32 3 0.01
33 16 0.04
34 106 0.24
35 19 0.04
36 111 0.25
37 37 0.08
38 39 0.09
39 85 0.19
40 4 0.01
41 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (35 bp):
TTACGATCACGACTTCATTTTTAAAGCTTGCTGAT
Found at i:5273746 original size:218 final size:216
Alignment explanation
Indices: 5273359--5273942 Score: 726
Period size: 218 Copynumber: 2.7 Consensus size: 216
5273349 TTACAGTTCA
* * * * * *
5273359 CTGATTTCCAATCACGATTGTCATTTTTAAAGCTTGTTGATTTACGATCATGGCTTATTCTTACG
1 CTGATTTACAATCACGACTGTCATTTTTAAAGCTCGTTGATTTACAATCACGACTTATTCTTACG
* * * * * * *
5273424 ATCCACTAATTTATTATCACAACCTTCGGTTTTCTAACAGTTCATTAATTTACGATCACGACTAT
66 -T-CGCTGATTTATAATCACGACCTTCGGTTTTCTAACAATTCGTTAATTTACGATCACGACTGT
*
5273489 CATTTTTAAAGCTCGTTGATTTACAATCATGGCTTATTCTTACAATACGCTAATTTACAATCACA
129 CATTTTTAAAGCTCGTTGATTTACAATCACGGCTTATTCTTACAATACGCTAATTTACAATCACA
*
5273554 ACCTTCGATTTTCTAACAGTTTG
194 ACCTTCGATTTTCTAACAATTTG
*
5273577 CTGATTTACAATCACAACTGTCATTTTTAAAGCTCGTTGATTTACAATCACGACTTATTCTTACG
1 CTGATTTACAATCACGACTGTCATTTTTAAAGCTCGTTGATTTACAATCACGACTTATTCTTAC-
* * * *
5273642 GTCTGCTGATTTATGATCACGACCTTTGGTTTTCTAACAATTCGTTGATTTACGATCACGATTGT
65 GTC-GCTGATTTATAATCACGACCTTCGGTTTTCTAACAATTCGTTAATTTACGATCACGACTGT
* * * * * * * *
5273707 CATTTTTAAAGCTTGCTGATTTACGATCACGGTTTATTCTTACGATTCGTTGATTTACAATCACA
129 CATTTTTAAAGCTCGTTGATTTACAATCACGGCTTATTCTTACAATACGCTAATTTACAATCACA
* * *
5273772 ATCTTCGATTTTCTAGCAATTTT
194 ACCTTCGATTTTCTAACAATTTG
* * ** *
5273795 CTGAGTTACGATCACGACTGTCATTTTTAAAGCTCGTTGATTTATTATCAC-AGTTTATTCTTAC
1 CTGATTTACAATCACGACTGTCATTTTTAAAGCTCGTTGATTTACAATCACGA-CTTATTCTTAC
* * * *
5273859 --CGTTGATTT-TCAATCACGACCTTCGATTTTCTAACAATTTGCTAATTTACGATCACGACTGT
65 GTCGCTGATTTAT-AATCACGACCTTCGGTTTTCTAACAATTCGTTAATTTACGATCACGACTGT
5273921 CATTTTTAAAGCTCGTTGATTT
129 CATTTTTAAAGCTCGTTGATTT
5273943 CTTCAACAAG
Statistics
Matches: 316, Mismatches: 46, Indels: 12
0.84 0.12 0.03
Matches are distributed among these distances:
213 1 0.00
214 71 0.22
215 1 0.00
217 2 0.01
218 240 0.76
219 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (216 bp):
CTGATTTACAATCACGACTGTCATTTTTAAAGCTCGTTGATTTACAATCACGACTTATTCTTACG
TCGCTGATTTATAATCACGACCTTCGGTTTTCTAACAATTCGTTAATTTACGATCACGACTGTCA
TTTTTAAAGCTCGTTGATTTACAATCACGGCTTATTCTTACAATACGCTAATTTACAATCACAAC
CTTCGATTTTCTAACAATTTG
Found at i:5276761 original size:62 final size:62
Alignment explanation
Indices: 5276685--5276871 Score: 374
Period size: 62 Copynumber: 3.0 Consensus size: 62
5276675 CACATAGGAT
5276685 CTAAGAAAAGTGAGTCCTAACCGACTCCAGAAATTTCCTTCGAGGGAGGGACCACAAGAAGA
1 CTAAGAAAAGTGAGTCCTAACCGACTCCAGAAATTTCCTTCGAGGGAGGGACCACAAGAAGA
5276747 CTAAGAAAAGTGAGTCCTAACCGACTCCAGAAATTTCCTTCGAGGGAGGGACCACAAGAAGA
1 CTAAGAAAAGTGAGTCCTAACCGACTCCAGAAATTTCCTTCGAGGGAGGGACCACAAGAAGA
5276809 CTAAGAAAAGTGAGTCCTAACCGACTCCAGAAATTTCCTTCGAGGGAGGGACCACAAGAAGA
1 CTAAGAAAAGTGAGTCCTAACCGACTCCAGAAATTTCCTTCGAGGGAGGGACCACAAGAAGA
5276871 C
1 C
5276872 CCAAGGCCAA
Statistics
Matches: 125, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 125 1.00
ACGTcount: A:0.37, C:0.23, G:0.24, T:0.16
Consensus pattern (62 bp):
CTAAGAAAAGTGAGTCCTAACCGACTCCAGAAATTTCCTTCGAGGGAGGGACCACAAGAAGA
Found at i:5278090 original size:4 final size:4
Alignment explanation
Indices: 5278081--5278131 Score: 59
Period size: 4 Copynumber: 12.8 Consensus size: 4
5278071 AGGAATCATG
* * *
5278081 TACA TACA TACA TGCA TACC TACA TGCA TACA TACA -AGCA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TA-CA TACA TACA
5278129 TAC
1 TAC
5278132 TCTGTTCTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
3 1 0.03
4 37 0.95
5 1 0.03
ACGTcount: A:0.43, C:0.27, G:0.06, T:0.24
Consensus pattern (4 bp):
TACA
Found at i:5278104 original size:12 final size:12
Alignment explanation
Indices: 5278083--5278129 Score: 76
Period size: 12 Copynumber: 3.9 Consensus size: 12
5278073 GAATCATGTA
5278083 CATACATACATG
1 CATACATACATG
*
5278095 CATACCTACATG
1 CATACATACATG
*
5278107 CATACATACAAG
1 CATACATACATG
5278119 CATACATACAT
1 CATACATACAT
5278130 ACTCTGTTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.43, C:0.28, G:0.06, T:0.23
Consensus pattern (12 bp):
CATACATACATG
Found at i:5280047 original size:25 final size:25
Alignment explanation
Indices: 5280019--5280068 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
5280009 AACGTGCATC
5280019 CCTATTCAACTTTAAAATGCATACT
1 CCTATTCAACTTTAAAATGCATACT
5280044 CCTATTCAACTTTAAAATGCATACT
1 CCTATTCAACTTTAAAATGCATACT
5280069 TGATTATACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.36
Consensus pattern (25 bp):
CCTATTCAACTTTAAAATGCATACT
Found at i:5282781 original size:21 final size:21
Alignment explanation
Indices: 5282757--5282796 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
5282747 AATATGCATA
5282757 TAATGGGATTTGAATCCACAC
1 TAATGGGATTTGAATCCACAC
5282778 TAATGGGATTTGAATCCAC
1 TAATGGGATTTGAATCCAC
5282797 GTAAAACATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (21 bp):
TAATGGGATTTGAATCCACAC
Found at i:5284597 original size:31 final size:31
Alignment explanation
Indices: 5284562--5284654 Score: 125
Period size: 32 Copynumber: 3.0 Consensus size: 31
5284552 ATATATTTAT
* *
5284562 TTTTTTTAATTTTAAAATATTTTTTACATAC
1 TTTTTTTAATTTTAAAATATTTTTAAAATAC
*
5284593 TTTTTTTAAATCTTAAAATATTTTTAAAATAC
1 TTTTTTT-AATTTTAAAATATTTTTAAAATAC
*
5284625 TTTTTTTAATTTTTTAAA-ATTTTTAAAATA
1 TTTTTTTAA-TTTTAAAATATTTTTAAAATA
5284655 AAAATGGGCC
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
31 21 0.38
32 34 0.62
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (31 bp):
TTTTTTTAATTTTAAAATATTTTTAAAATAC
Found at i:5292197 original size:15 final size:15
Alignment explanation
Indices: 5292161--5292199 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
5292151 CTGCAAGTTT
*
5292161 CAAGAATATAATCAA
1 CAAGAATATCATCAA
*
5292176 C-AGAATATCATGAA
1 CAAGAATATCATCAA
5292190 CAAGAATATC
1 CAAGAATATC
5292200 CTCCAAAGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.54, C:0.15, G:0.10, T:0.21
Consensus pattern (15 bp):
CAAGAATATCATCAA
Found at i:5298154 original size:15 final size:15
Alignment explanation
Indices: 5298134--5298180 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
5298124 AATTGGGTTA
5298134 AGAAAATTATTTAAT
1 AGAAAATTATTTAAT
*
5298149 AGAAAAATTAATTAAT
1 AG-AAAATTATTTAAT
*
5298165 -TAAAATTAATTTAAT
1 AGAAAATT-ATTTAAT
5298180 A
1 A
5298181 AACAATATCT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
14 6 0.23
15 8 0.31
16 12 0.46
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.38
Consensus pattern (15 bp):
AGAAAATTATTTAAT
Found at i:5301101 original size:19 final size:19
Alignment explanation
Indices: 5301077--5301116 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
5301067 ATTCCAAAAA
*
5301077 TAATATT-ATTTTAATAGTT
1 TAATATTAAATTTAATA-TT
5301096 TAATATTAAATTTAATATT
1 TAATATTAAATTTAATATT
5301115 TA
1 TA
5301117 TCTTGTAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (19 bp):
TAATATTAAATTTAATATT
Found at i:5301303 original size:25 final size:25
Alignment explanation
Indices: 5301269--5301317 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
5301259 TGTAGAGAGA
5301269 AAATTCTCTAAAGAGATTATTTTAG
1 AAATTCTCTAAAGAGATTATTTTAG
* * * *
5301294 AAATTTTCTAGAGATATTTTTTTA
1 AAATTCTCTAAAGAGATTATTTTA
5301318 TTTACAACTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.47
Consensus pattern (25 bp):
AAATTCTCTAAAGAGATTATTTTAG
Found at i:5302168 original size:5 final size:5
Alignment explanation
Indices: 5302160--5302188 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
5302150 AAGTATAAAT
5302160 ATTAG ATTAG ATTAG ATTAG ATTAG ATTA
1 ATTAG ATTAG ATTAG ATTAG ATTAG ATTA
5302189 TAAAAGATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.17, T:0.41
Consensus pattern (5 bp):
ATTAG
Found at i:5303275 original size:25 final size:25
Alignment explanation
Indices: 5303224--5303325 Score: 81
Period size: 22 Copynumber: 4.3 Consensus size: 25
5303214 ACTTTAGCGC
* **
5303224 GCTCTCTGATTATTAGCACGTTGGT
1 GCTCTCTGATTACTAGCACGTCAGT
*
5303249 GCTCTCTGATTACTAGCATGTCAGT
1 GCTCTCTGATTACTAGCACGTCAGT
* * *
5303274 GCTCTCCG-TT--TAGCACATCTGT
1 GCTCTCTGATTACTAGCACGTCAGT
* *
5303296 GCTCTCTG--TA-TAGCACTTTAGT
1 GCTCTCTGATTACTAGCACGTCAGT
5303318 GCTCTCTG
1 GCTCTCTG
5303326 TTCATTAGTG
Statistics
Matches: 64, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
21 1 0.02
22 33 0.52
24 2 0.03
25 28 0.44
ACGTcount: A:0.16, C:0.25, G:0.21, T:0.38
Consensus pattern (25 bp):
GCTCTCTGATTACTAGCACGTCAGT
Found at i:5308393 original size:27 final size:27
Alignment explanation
Indices: 5308330--5308399 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
5308320 TCATTAAGTA
* *
5308330 TTCACCACAAAGGCTTTCCTTTCAGAG
1 TTCACCACAAAGGCTGTCCTTTAAGAG
* *
5308357 TCTCAACACAAAGG-TGTCTTTTAAGAGG
1 T-TCACCACAAAGGCTGTCCTTTAAGA-G
5308385 TTCACCACAAAGGCT
1 TTCACCACAAAGGCT
5308400 TACCCTTCTA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
27 21 0.60
28 14 0.40
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (27 bp):
TTCACCACAAAGGCTGTCCTTTAAGAG
Found at i:5309839 original size:25 final size:25
Alignment explanation
Indices: 5309804--5309871 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 25
5309794 AAACATAACA
* *
5309804 TAAACACTTAATTCATATCCTTGAT
1 TAAACACTTAATTCATATACTTCAT
* * *
5309829 TAAACAATTAATTTATATATTTCAT
1 TAAACACTTAATTCATATACTTCAT
*
5309854 TTAACACTTAATTCATAT
1 TAAACACTTAATTCATAT
5309872 GTATTACTAA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.40, C:0.15, G:0.01, T:0.44
Consensus pattern (25 bp):
TAAACACTTAATTCATATACTTCAT
Found at i:5310026 original size:14 final size:15
Alignment explanation
Indices: 5310007--5310036 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5309997 CTCCTAAATT
5310007 ATAACAG-AACTCTA
1 ATAACAGAAACTCTA
5310021 ATAACAGAAACTCTA
1 ATAACAGAAACTCTA
5310036 A
1 A
5310037 GAACTCCAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.53, C:0.20, G:0.07, T:0.20
Consensus pattern (15 bp):
ATAACAGAAACTCTA
Found at i:5327561 original size:19 final size:21
Alignment explanation
Indices: 5327537--5327577 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5327527 AACTTTTTTC
5327537 CAAATTA-T-ATGAATTGTTT
1 CAAATTAGTCATGAATTGTTT
*
5327556 CAAATTAGTCCTGAATTGTTT
1 CAAATTAGTCATGAATTGTTT
5327577 C
1 C
5327578 CGAACTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 1 0.05
21 11 0.58
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (21 bp):
CAAATTAGTCATGAATTGTTT
Found at i:5331833 original size:19 final size:20
Alignment explanation
Indices: 5331809--5331858 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
5331799 AAATTAAGTT
5331809 AAATTTTACTTTTCCTC-CA
1 AAATTTTACTTTTCCTCACA
5331828 AAATTTTTAC--TTCCTCTACA
1 AAA-TTTTACTTTTCCTC-ACA
5331848 AAATTTTACTT
1 AAATTTTACTT
5331859 CCTCAAACCC
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
18 6 0.23
19 9 0.35
20 11 0.42
ACGTcount: A:0.30, C:0.22, G:0.00, T:0.48
Consensus pattern (20 bp):
AAATTTTACTTTTCCTCACA
Found at i:5331849 original size:20 final size:19
Alignment explanation
Indices: 5331809--5331862 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
5331799 AAATTAAGTT
5331809 AAATTTTACTTTTCCTC--CA
1 AAATTTTAC--TTCCTCTACA
5331828 AAATTTTTACTTCCTCTACA
1 AAA-TTTTACTTCCTCTACA
5331848 AAATTTTACTTCCTC
1 AAATTTTACTTCCTC
5331863 AAACCCCCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
18 6 0.19
19 15 0.47
20 11 0.34
ACGTcount: A:0.28, C:0.26, G:0.00, T:0.46
Consensus pattern (19 bp):
AAATTTTACTTCCTCTACA
Found at i:5331921 original size:17 final size:20
Alignment explanation
Indices: 5331884--5331920 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5331874 AACTTTTTAC
5331884 CTTTTACTTTCTCTCCAAAA
1 CTTTTACTTTCTCTCCAAAA
5331904 CTTTTAC-TTCTC-CCAAA
1 CTTTTACTTTCTCTCCAAA
5331921 CCCTCAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 5 0.29
20 7 0.41
ACGTcount: A:0.24, C:0.32, G:0.00, T:0.43
Consensus pattern (20 bp):
CTTTTACTTTCTCTCCAAAA
Found at i:5331929 original size:54 final size:54
Alignment explanation
Indices: 5331832--5331969 Score: 174
Period size: 53 Copynumber: 2.6 Consensus size: 54
5331822 CCTCCAAAAT
* * *
5331832 TTTTACTTCCTCTACAAAA-TTTTACTTCCTCAAACCCCCCAAAACTTTTTACC
1 TTTTACTTTCTCTCCAAAACTTTTACTTCCCCAAACCCCCCAAAACTTTTTACC
* *
5331885 TTTTACTTTCTCTCCAAAACTTTTACTTCTCCCAAA-CCCTCAAAACTTTTTTCC
1 TTTTACTTTCTCTCCAAAACTTTTACTTC-CCCAAACCCCCCAAAACTTTTTACC
* * *
5331939 TTTTA-TTTTTCCCCCAAACTTTTACTTCCCC
1 TTTTACTTTCTCTCCAAAACTTTTACTTCCCC
5331970 CTCAAAAATT
Statistics
Matches: 75, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
52 3 0.04
53 37 0.49
54 30 0.40
55 5 0.07
ACGTcount: A:0.24, C:0.34, G:0.00, T:0.42
Consensus pattern (54 bp):
TTTTACTTTCTCTCCAAAACTTTTACTTCCCCAAACCCCCCAAAACTTTTTACC
Found at i:5331975 original size:19 final size:19
Alignment explanation
Indices: 5331949--5331990 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
5331939 TTTTATTTTT
*
5331949 CCCCC-AAACTTTTACTTC
1 CCCCCAAAAATTTTACTTC
5331967 CCCCTCAAAAATTTTACTTC
1 CCCC-CAAAAATTTTACTTC
5331987 CCCC
1 CCCC
5331991 AAATCCCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 4 0.19
19 1 0.05
20 16 0.76
ACGTcount: A:0.24, C:0.45, G:0.00, T:0.31
Consensus pattern (19 bp):
CCCCCAAAAATTTTACTTC
Found at i:5332456 original size:19 final size:19
Alignment explanation
Indices: 5332432--5332469 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5332422 AAAGCTAATA
*
5332432 ACAAATTTGATTACGGTAG
1 ACAAATTTGATTAAGGTAG
5332451 ACAAATTTGATTAAGGTAG
1 ACAAATTTGATTAAGGTAG
5332470 GTGACAGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.32
Consensus pattern (19 bp):
ACAAATTTGATTAAGGTAG
Found at i:5333224 original size:33 final size:35
Alignment explanation
Indices: 5333187--5333283 Score: 89
Period size: 33 Copynumber: 2.8 Consensus size: 35
5333177 ATGGTTAGAT
5333187 TTAAATATTTAAAATATAATTTATATATT-C-TAA
1 TTAAATATTTAAAATATAATTTATATATTGCTTAA
* *
5333220 TTAAAT-TTTATAA-ATAATTAATATTTATTGCTTAA
1 TTAAATATTTAAAATATAATT--TATATATTGCTTAA
*
5333255 --AAATATTTAAAATTTATATTTCATATATT
1 TTAAATATTTAAAATATA-ATTT-ATATATT
5333284 AAAATATTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
31 6 0.12
32 6 0.12
33 17 0.33
34 8 0.16
35 11 0.22
36 3 0.06
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (35 bp):
TTAAATATTTAAAATATAATTTATATATTGCTTAA
Found at i:5335395 original size:6 final size:6
Alignment explanation
Indices: 5335384--5335417 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
5335374 TTTGGCCTCA
5335384 TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTT
1 TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTT
5335418 ACTGTTTGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (6 bp):
TCTTCC
Found at i:5335799 original size:3 final size:3
Alignment explanation
Indices: 5335791--5335823 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
5335781 CAATTCAGGC
5335791 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
5335824 GGTTGTGCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:5350325 original size:48 final size:48
Alignment explanation
Indices: 5350243--5350336 Score: 138
Period size: 48 Copynumber: 2.0 Consensus size: 48
5350233 TTTCTTGGCT
* *
5350243 TAAAAACGCCTAAGTCAGCCTAACTTCCACCAATAATGGATTCAACCG
1 TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
5350291 TAAAAACGCCTAAGTCAG-CTCAAC-TCGCAACAATAAAGGATTCAAC
1 TAAAAACGCCTAAGTCAGCCT-AACTTC-CAACAATAAAGGATTCAAC
5350337 AGAATTCCCT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
47 4 0.10
48 38 0.90
ACGTcount: A:0.40, C:0.28, G:0.13, T:0.19
Consensus pattern (48 bp):
TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
Found at i:5351032 original size:99 final size:99
Alignment explanation
Indices: 5350861--5351058 Score: 378
Period size: 99 Copynumber: 2.0 Consensus size: 99
5350851 GCCCGTGACA
*
5350861 TTCTCCCCCACCCATTCTCGCAACGCCCTCGTTGCGACTTCTGAATGGCACTGACTTGATTCGCC
1 TTCTCCCCCACCCATTCTCGCAACGCCCTCGTTGCGACTTCTGAATGGCACAGACTTGATTCGCC
5350926 TCGGTCTCGTCTCGTCGCCTTAGCCTTTCCCTTT
66 TCGGTCTCGTCTCGTCGCCTTAGCCTTTCCCTTT
5350960 TTCTCCCCCACCCATTCTCGCAACGCCCTCGTTGCGACTTCTGAATGGCACAGACTTGATTCGCC
1 TTCTCCCCCACCCATTCTCGCAACGCCCTCGTTGCGACTTCTGAATGGCACAGACTTGATTCGCC
*
5351025 TCGGTCTCGTCTCGTCGTCTTAGCCTTTCCCTTT
66 TCGGTCTCGTCTCGTCGCCTTAGCCTTTCCCTTT
5351059 CTTTGGGATT
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
99 97 1.00
ACGTcount: A:0.12, C:0.39, G:0.17, T:0.32
Consensus pattern (99 bp):
TTCTCCCCCACCCATTCTCGCAACGCCCTCGTTGCGACTTCTGAATGGCACAGACTTGATTCGCC
TCGGTCTCGTCTCGTCGCCTTAGCCTTTCCCTTT
Found at i:5353243 original size:17 final size:19
Alignment explanation
Indices: 5353207--5353250 Score: 65
Period size: 17 Copynumber: 2.4 Consensus size: 19
5353197 TTTGAAAATG
5353207 TAAAACTAAATTTAAGTAAA
1 TAAAA-TAAATTTAAGTAAA
5353227 TAAAATAAA-TT-AGTAAA
1 TAAAATAAATTTAAGTAAA
5353244 TAAAATA
1 TAAAATA
5353251 TTTTTTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.54
18 2 0.08
19 4 0.17
20 5 0.21
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (19 bp):
TAAAATAAATTTAAGTAAA
Found at i:5354083 original size:23 final size:23
Alignment explanation
Indices: 5354053--5354127 Score: 123
Period size: 23 Copynumber: 3.3 Consensus size: 23
5354043 TAGATTTTTC
5354053 CTAAATATTATCATTAAATAATT
1 CTAAATATTATCATTAAATAATT
*
5354076 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCATTAAATAATT
*
5354099 CTAAGTATTATCATTAAATAATT
1 CTAAATATTATCATTAAATAATT
*
5354122 CAAAAT
1 CTAAAT
5354128 TTAAAAATCA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.48, C:0.11, G:0.01, T:0.40
Consensus pattern (23 bp):
CTAAATATTATCATTAAATAATT
Found at i:5360825 original size:19 final size:18
Alignment explanation
Indices: 5360795--5360843 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
5360785 TTCGAAAATG
5360795 TAAAAGTAAATTTAAGTAAA
1 TAAAA-TAAATTT-AGTAAA
*
5360815 TAAAATAAA-TTGGTAAA
1 TAAAATAAATTTAGTAAA
*
5360832 TAAAATATATTT
1 TAAAATAAATTT
5360844 TTAAAAGCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 13 0.50
18 4 0.15
19 4 0.15
20 5 0.19
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (18 bp):
TAAAATAAATTTAGTAAA
Found at i:5361684 original size:13 final size:13
Alignment explanation
Indices: 5361666--5361708 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
5361656 TAGATTTTTT
5361666 CTAAATATTATCA
1 CTAAATATTATCA
*
5361679 CTAAATA--AT-T
1 CTAAATATTATCA
5361689 CTAAATATTATCA
1 CTAAATATTATCA
5361702 CTAAATA
1 CTAAATA
5361709 ATTCAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 7 0.28
11 2 0.08
12 2 0.08
13 14 0.56
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:5361691 original size:23 final size:23
Alignment explanation
Indices: 5361664--5361717 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
5361654 GCTAGATTTT
5361664 TTCTAAATATTATCACTAAATAA
1 TTCTAAATATTATCACTAAATAA
5361687 TTCTAAATATTATCACTAAATAA
1 TTCTAAATATTATCACTAAATAA
*
5361710 TTCAAAAT
1 TTCTAAAT
5361718 TTAAAAATCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (23 bp):
TTCTAAATATTATCACTAAATAA
Found at i:5362871 original size:21 final size:21
Alignment explanation
Indices: 5362832--5362871 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5362822 TTTTCGAGTT
*
5362832 GAGTCGAGTGAAATGAAATTC
1 GAGTCGAGTGAAATCAAATTC
5362853 GAGTCGAGTCG-AATCAAAT
1 GAGTCGAGT-GAAATCAAAT
5362872 CAAGTAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.38, C:0.12, G:0.28, T:0.23
Consensus pattern (21 bp):
GAGTCGAGTGAAATCAAATTC
Found at i:5372900 original size:12 final size:11
Alignment explanation
Indices: 5372873--5372913 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
5372863 GAAAATTTTA
5372873 TTTTAAAATAT
1 TTTTAAAATAT
5372884 TTTTAAAATACT
1 TTTTAAAATA-T
5372896 TTTT--AA-AT
1 TTTTAAAATAT
5372904 TTTTAAAATA
1 TTTTAAAATA
5372914 AATTTTTGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
8 5 0.19
9 1 0.04
10 4 0.15
11 11 0.42
12 5 0.19
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:5372919 original size:20 final size:20
Alignment explanation
Indices: 5372882--5372919 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5372872 ATTTTAAAAT
**
5372882 ATTTTTAAAATACTTTTTAA
1 ATTTTTAAAATAAATTTTAA
5372902 ATTTTTAAAATAAATTTT
1 ATTTTTAAAATAAATTTT
5372920 TGGTATTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (20 bp):
ATTTTTAAAATAAATTTTAA
Found at i:5375682 original size:20 final size:20
Alignment explanation
Indices: 5375641--5375683 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
5375631 AACTATGTTT
**
5375641 ATTTAAAATAAAAATATTAA
1 ATTTAAAATAAAAATAGAAA
*
5375661 ATTTAAACTAAAAATAGAAA
1 ATTTAAAATAAAAATAGAAA
5375681 ATT
1 ATT
5375684 ATAATATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (20 bp):
ATTTAAAATAAAAATAGAAA
Found at i:5375879 original size:25 final size:25
Alignment explanation
Indices: 5375851--5375929 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 25
5375841 ATTAAATATA
*
5375851 TAAAAATGTATATAATATATAATTT
1 TAAAAATGTATAAAATATATAATTT
* *
5375876 TAAAAAATGTTTAAGAAT-TAT-TTTT
1 T-AAAAATGTATAA-AATATATAATTT
*
5375901 TATAAAAT-TCTAAAATATATAATTT
1 TA-AAAATGTATAAAATATATAATTT
5375926 TAAA
1 TAAA
5375930 TTTTAAAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
23 3 0.07
24 10 0.23
25 15 0.34
26 13 0.30
27 3 0.07
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (25 bp):
TAAAAATGTATAAAATATATAATTT
Found at i:5376872 original size:20 final size:20
Alignment explanation
Indices: 5376847--5376910 Score: 94
Period size: 20 Copynumber: 3.2 Consensus size: 20
5376837 TTCTAATTAG
5376847 TAAATTTTTTTTTAAAATAT
1 TAAATTTTTTTTTAAAATAT
*
5376867 TAAATTTTATTTTAAAATAT
1 TAAATTTTTTTTTAAAATAT
*
5376887 ATAAA-GTTTTTTTAAAATAT
1 -TAAATTTTTTTTTAAAATAT
5376907 TAAA
1 TAAA
5376911 ATGTTATAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
19 4 0.10
20 32 0.80
21 4 0.10
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
TAAATTTTTTTTTAAAATAT
Found at i:5376872 original size:28 final size:27
Alignment explanation
Indices: 5376813--5376872 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
5376803 ATTTGTTTAA
5376813 AAATTGTAAATTTTATTTTAAAAATTC
1 AAATTGTAAATTTTATTTTAAAAATTC
* *
5376840 TAATTAGTAAATTTTTTTTTAAAATATT-
1 AAATT-GTAAATTTTATTTTAAAA-ATTC
5376868 AAATT
1 AAATT
5376873 TTATTTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 4 0.14
28 21 0.75
29 3 0.11
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (27 bp):
AAATTGTAAATTTTATTTTAAAAATTC
Found at i:5377014 original size:17 final size:18
Alignment explanation
Indices: 5376964--5377024 Score: 70
Period size: 17 Copynumber: 3.3 Consensus size: 18
5376954 AAAATGTAAA
*
5376964 AAAAATACTAAATAATTTT
1 AAAAATATTAAA-AATTTT
*
5376983 GAAAAACATTAAAAATTTT
1 -AAAAATATTAAAAATTTT
*
5377002 AAAAATATT-AAAATTGT
1 AAAAATATTAAAAATTTT
5377019 AAAAAT
1 AAAAAT
5377025 TATAAGATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
17 13 0.35
18 8 0.22
19 6 0.16
20 10 0.27
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (18 bp):
AAAAATATTAAAAATTTT
Found at i:5377054 original size:18 final size:19
Alignment explanation
Indices: 5377021--5377056 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
5377011 AAAATTGTAA
5377021 AAATTATAAGATTTTTTTT
1 AAATTATAAGATTTTTTTT
*
5377040 AAATTTTAA-ATTTTTTT
1 AAATTATAAGATTTTTTT
5377057 AAAAATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (19 bp):
AAATTATAAGATTTTTTTT
Found at i:5377062 original size:19 final size:20
Alignment explanation
Indices: 5377018--5377065 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
5377008 ATTAAAATTG
5377018 TAAAAATTATAAGATTTTTT
1 TAAAAATTATAAGATTTTTT
* *
5377038 T-TAAATTTTAA-ATTTTTT
1 TAAAAATTATAAGATTTTTT
5377056 TAAAAATTAT
1 TAAAAATTAT
5377066 TATAATAAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 8 0.35
19 14 0.61
20 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
TAAAAATTATAAGATTTTTT
Found at i:5377956 original size:19 final size:20
Alignment explanation
Indices: 5377909--5377970 Score: 67
Period size: 19 Copynumber: 3.1 Consensus size: 20
5377899 AATATAAAAT
*
5377909 TTTATATATTTTAATTTGTAA
1 TTTATATATTTTAA-TTATAA
5377930 TTGT-TATATTTTAA-TATAA
1 TT-TATATATTTTAATTATAA
*
5377949 TTTATATATTTAAATTA-AA
1 TTTATATATTTTAATTATAA
5377968 TTT
1 TTT
5377971 TGTAAATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
18 1 0.03
19 20 0.56
20 2 0.06
21 12 0.33
22 1 0.03
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (20 bp):
TTTATATATTTTAATTATAA
Found at i:5379783 original size:13 final size:13
Alignment explanation
Indices: 5379765--5379789 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5379755 AACCATCTAA
5379765 CATAGCCTGGAAT
1 CATAGCCTGGAAT
5379778 CATAGCCTGGAA
1 CATAGCCTGGAA
5379790 ATTTGGTGCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.20
Consensus pattern (13 bp):
CATAGCCTGGAAT
Found at i:5380090 original size:14 final size:14
Alignment explanation
Indices: 5380071--5380098 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5380061 TTGCCTTTAA
5380071 AAATAAGTTAATTC
1 AAATAAGTTAATTC
5380085 AAATAAGTTAATTC
1 AAATAAGTTAATTC
5380099 TTTTTAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (14 bp):
AAATAAGTTAATTC
Found at i:5380925 original size:58 final size:59
Alignment explanation
Indices: 5380855--5380992 Score: 224
Period size: 59 Copynumber: 2.4 Consensus size: 59
5380845 GTTAAACATT
****
5380855 ATTTATAACATTGTCAAATTTATAATTT-AAAAAATTATAAAAAATAGAAATAAATTTT
1 ATTTATAACATTGTCAAATTTATAATTTAAAAAAATTATAAAAAATAGAAATAAAAAAA
*
5380913 TTTTATAACATTGTCAAATTTATAATTTAAAAAAATTATAAAAAATAGAAATAAAAAAA
1 ATTTATAACATTGTCAAATTTATAATTTAAAAAAATTATAAAAAATAGAAATAAAAAAA
5380972 ATTTATAACATTGTCAAATTT
1 ATTTATAACATTGTCAAATTT
5380993 TTTTGTTTAT
Statistics
Matches: 73, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
58 27 0.37
59 46 0.63
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (59 bp):
ATTTATAACATTGTCAAATTTATAATTTAAAAAAATTATAAAAAATAGAAATAAAAAAA
Found at i:5383588 original size:14 final size:14
Alignment explanation
Indices: 5383565--5383604 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
5383555 ACAGAAAAGT
*
5383565 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
5383579 AAATCATTTTACGG
1 AAAACATTTTACAG
5383593 AAAACATTTTAC
1 AAAACATTTTAC
5383605 TGCCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:5383590 original size:34 final size:35
Alignment explanation
Indices: 5383530--5383596 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
5383520 CAAACACCAG
* *
5383530 AAAATATTTTCCAGTAAGTCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
5383565 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
5383597 CATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:5384334 original size:12 final size:12
Alignment explanation
Indices: 5384319--5384360 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
5384309 GTTCAATTAT
*
5384319 ATGTTCATGAAC
1 ATGTTCGTGAAC
**
5384331 ATGTTCGTTTA-
1 ATGTTCGTGAAC
5384342 ATGTTCGTGAAC
1 ATGTTCGTGAAC
5384354 ATGTTCG
1 ATGTTCG
5384361 ATTAAGTTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.40
Consensus pattern (12 bp):
ATGTTCGTGAAC
Found at i:5384352 original size:23 final size:23
Alignment explanation
Indices: 5384296--5384365 Score: 104
Period size: 23 Copynumber: 3.0 Consensus size: 23
5384286 TTATTAATGT
*
5384296 TGTTCGTGAACATGTTCAATTATA
1 TGTTCGTGAACATGTTCGATTA-A
* *
5384320 TGTTCATGAACATGTTCGTTTAA
1 TGTTCGTGAACATGTTCGATTAA
5384343 TGTTCGTGAACATGTTCGATTAA
1 TGTTCGTGAACATGTTCGATTAA
5384366 GTTAAATGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
23 22 0.54
24 19 0.46
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.41
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCGATTAA
Found at i:5384375 original size:23 final size:23
Alignment explanation
Indices: 5384296--5384380 Score: 100
Period size: 23 Copynumber: 3.7 Consensus size: 23
5384286 TTATTAATGT
* *
5384296 TGTTCGTGAACATGTTCAATTATA
1 TGTTCATGAACATGTTCGATTA-A
*
5384320 TGTTCATGAACATGTTCGTTTAA
1 TGTTCATGAACATGTTCGATTAA
*
5384343 TGTTCGTGAACATGTTCGATTAA
1 TGTTCATGAACATGTTCGATTAA
*
5384366 -GTTAAATGAACATGT
1 TGTT-CATGAACATGT
5384381 CCGTGAATAT
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
22 3 0.06
23 31 0.58
24 19 0.36
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (23 bp):
TGTTCATGAACATGTTCGATTAA
Found at i:5391051 original size:19 final size:18
Alignment explanation
Indices: 5391014--5391064 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
5391004 TCTCGCTTAA
*
5391014 ATTGTTTTATATAAGATT
1 ATTGTTTTATATAAAATT
*
5391032 ATTGTTTATTTATAAAATT
1 ATTGTTT-TATATAAAATT
*
5391051 ATTATTTTA-ATAAA
1 ATTGTTTTATATAAA
5391065 TAAATTGTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
17 5 0.18
18 8 0.29
19 15 0.54
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (18 bp):
ATTGTTTTATATAAAATT
Found at i:5397174 original size:13 final size:11
Alignment explanation
Indices: 5397146--5397179 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
5397136 ATTTTTTTCT
5397146 CATATATTGTA
1 CATATATTGTA
5397157 CATATATTGTA
1 CATATATTGTA
5397168 CATATATTGTA
1 CATATATTGTA
5397179 C
1 C
5397180 TAATTCCTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (11 bp):
CATATATTGTA
Found at i:5398421 original size:20 final size:20
Alignment explanation
Indices: 5398396--5398435 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
5398386 AATATTTTCC
* *
5398396 AGTAAATCATTTTACAGAAA
1 AGTAAAACACTTTACAGAAA
*
5398416 AGTAAAACACTTTCCAGAAA
1 AGTAAAACACTTTACAGAAA
5398436 TCATTTTACG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.15, G:0.10, T:0.25
Consensus pattern (20 bp):
AGTAAAACACTTTACAGAAA
Found at i:5409427 original size:27 final size:27
Alignment explanation
Indices: 5409396--5409490 Score: 95
Period size: 27 Copynumber: 3.5 Consensus size: 27
5409386 GAGGATTTTT
*
5409396 TGTGTTTACTATCCTGATGGATCATCC
1 TGTGTTTACTATCCTGATGGATTATCC
* * * *
5409423 CGTGTTTACTGTCCT-AGCGGATTATCT
1 TGTGTTTACTATCCTGA-TGGATTATCC
*
5409450 TGTGTTTACTATCAC-GATAGATTATCC
1 TGTGTTTACTATC-CTGATGGATTATCC
*
5409477 TGTGTTTATTATCC
1 TGTGTTTACTATCC
5409491 CAGCAGACTA
Statistics
Matches: 54, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
26 2 0.04
27 50 0.93
28 2 0.04
ACGTcount: A:0.19, C:0.20, G:0.18, T:0.43
Consensus pattern (27 bp):
TGTGTTTACTATCCTGATGGATTATCC
Found at i:5411019 original size:27 final size:27
Alignment explanation
Indices: 5410980--5411041 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
5410970 CACACAGGAA
5410980 AAATGGAAACTTTTGTGACAATCTATG
1 AAATGGAAACTTTTGTGACAATCTATG
* * * *
5411007 AAATTGAAGCTTTTGTGGCGATCTATGG
1 AAATGGAAACTTTTGTGACAATCTAT-G
5411035 AAA-GGAA
1 AAATGGAA
5411042 TGCCTTCGTG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
27 25 0.86
28 4 0.14
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.31
Consensus pattern (27 bp):
AAATGGAAACTTTTGTGACAATCTATG
Found at i:5421039 original size:30 final size:30
Alignment explanation
Indices: 5420993--5421055 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
5420983 ACTTAACAAG
*
5420993 CAAATGTCTCTAAAATAATAACAAAATTAA
1 CAAACGTCTCTAAAATAATAACAAAATTAA
* *
5421023 CAAACGTCTTTAAAATAATAATAAAATTAA
1 CAAACGTCTCTAAAATAATAACAAAATTAA
5421053 CAA
1 CAA
5421056 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.57, C:0.13, G:0.03, T:0.27
Consensus pattern (30 bp):
CAAACGTCTCTAAAATAATAACAAAATTAA
Found at i:5428122 original size:25 final size:25
Alignment explanation
Indices: 5428092--5428162 Score: 124
Period size: 25 Copynumber: 2.8 Consensus size: 25
5428082 GTATTAGTAG
5428092 TTTAATGAAATTTCAATTTTTTATT
1 TTTAATGAAATTTCAATTTTTTATT
5428117 TTTAATGAAATTTCAATTTTTTATT
1 TTTAATGAAATTTCAATTTTTTATT
* *
5428142 TTTAATAAAATTTCAAATTTT
1 TTTAATGAAATTTCAATTTTT
5428163 GATAAAATTG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.35, C:0.04, G:0.03, T:0.58
Consensus pattern (25 bp):
TTTAATGAAATTTCAATTTTTTATT
Found at i:5428254 original size:21 final size:19
Alignment explanation
Indices: 5428214--5428253 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
5428204 TTTTTTTTAC
5428214 TAATGGTTTTTTAGATTTT
1 TAATGGTTTTTTAGATTTT
5428233 TAATGGTTGATTTTA-ATTTT
1 TAATGGTT--TTTTAGATTTT
5428253 T
1 T
5428254 TTAATTTGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.42
20 6 0.32
21 5 0.26
ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (19 bp):
TAATGGTTTTTTAGATTTT
Found at i:5440272 original size:39 final size:41
Alignment explanation
Indices: 5440155--5440338 Score: 190
Period size: 40 Copynumber: 4.6 Consensus size: 41
5440145 GCTCCTCGTT
* * *
5440155 CAAATGCCTTCGGGACATAGCTCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAATCTCGCA
* *
5440195 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAA-CTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAATCTCGCA
5440235 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGT-ATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAATCTCGCA
* * *
5440274 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGTAATC-TCGCA
5440315 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
5440339 CATCATTCAA
Statistics
Matches: 127, Mismatches: 8, Indels: 19
0.82 0.05 0.12
Matches are distributed among these distances:
38 3 0.02
39 48 0.38
40 65 0.51
41 11 0.09
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (41 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAATCTCGCA
Found at i:5440273 original size:79 final size:82
Alignment explanation
Indices: 5440155--5440338 Score: 215
Period size: 79 Copynumber: 2.3 Consensus size: 82
5440145 GCTCCTCGTT
* * *
5440155 CAAATGCCTTCGGGACATAGCTCGG-TTATAGTAATTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAATTCGCACAAATGCCTTC-GGATCTTAACCC
*
5440218 GGAT-TTAGTAAC-TCGCA
65 GGATATT-GTAACTTAGCA
**
5440235 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ATCTCGCACAAATGCCTTCGGATCTTAGTCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAAT-TCGCACAAATGCCTTCGGATCTTAACCC
*
5440297 GGATATTGTCACTTAGCA
65 GGATATTGTAACTTAGCA
5440315 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
5440339 CATCATTCAA
Statistics
Matches: 91, Mismatches: 7, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
78 14 0.15
79 55 0.60
80 22 0.24
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAATTCGCACAAATGCCTTCGGATCTTAACCCG
GATATTGTAACTTAGCA
Found at i:5447911 original size:31 final size:31
Alignment explanation
Indices: 5447876--5447956 Score: 117
Period size: 31 Copynumber: 2.6 Consensus size: 31
5447866 TGTATATGTT
*
5447876 TTATACATTGCCGAATTTGATTTGTATATAG
1 TTATACATTGTCGAATTTGATTTGTATATAG
* *
5447907 TTATACATTGTCAAATTTGATTTGTATATGG
1 TTATACATTGTCGAATTTGATTTGTATATAG
* *
5447938 ATATTCATTGTCGAATTTG
1 TTATACATTGTCGAATTTG
5447957 TTGTCAAATT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.28, C:0.09, G:0.16, T:0.47
Consensus pattern (31 bp):
TTATACATTGTCGAATTTGATTTGTATATAG
Found at i:5447975 original size:43 final size:43
Alignment explanation
Indices: 5447914--5447999 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
5447904 TAGTTATACA
5447914 TTGTCAAATTTGATTTGTATATGGATATTCATTGTCGAATTTG
1 TTGTCAAATTTGATTTGTATATGGATATTCATTGTCGAATTTG
5447957 TTGTCAAATTTGATTTGTATATGGATATTCATTGTCGAATTTG
1 TTGTCAAATTTGATTTGTATATGGATATTCATTGTCGAATTTG
5448000 ATTTGTATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.26, C:0.07, G:0.19, T:0.49
Consensus pattern (43 bp):
TTGTCAAATTTGATTTGTATATGGATATTCATTGTCGAATTTG
Found at i:5447978 original size:74 final size:74
Alignment explanation
Indices: 5447889--5448030 Score: 212
Period size: 74 Copynumber: 1.9 Consensus size: 74
5447879 TACATTGCCG
* * * **
5447889 AATTTGATTTGTATATAGTTATACATTGTCAAATTTGATTTGTATATGGATATTCATTGTCGAAT
1 AATTTGATTTGTATATAGATATACATTGTCAAATTTGATTTGTATATAGATATACATTACCGAAT
5447954 TTGTTGTCA
66 TTGTTGTCA
* * *
5447963 AATTTGATTTGTATATGGATATTCATTGTCGAATTTGATTTGTATATAGATATACATTACCGAAT
1 AATTTGATTTGTATATAGATATACATTGTCAAATTTGATTTGTATATAGATATACATTACCGAAT
5448028 TTG
66 TTG
5448031 ATTCGTATAT
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
74 60 1.00
ACGTcount: A:0.30, C:0.07, G:0.16, T:0.47
Consensus pattern (74 bp):
AATTTGATTTGTATATAGATATACATTGTCAAATTTGATTTGTATATAGATATACATTACCGAAT
TTGTTGTCA
Found at i:5447998 original size:31 final size:31
Alignment explanation
Indices: 5447957--5448065 Score: 141
Period size: 31 Copynumber: 3.5 Consensus size: 31
5447947 GTCGAATTTG
*
5447957 TTGTCAAATTTGATTTGTATATGGATATTCA
1 TTGTCGAATTTGATTTGTATATGGATATTCA
* *
5447988 TTGTCGAATTTGATTTGTATATAGATATACA
1 TTGTCGAATTTGATTTGTATATGGATATTCA
** *
5448019 TTACCGAATTTGATTCGTATATGGATATAT-A
1 TTGTCGAATTTGATTTGTATATGGATAT-TCA
5448050 TTGTCGAA-TTGATTTG
1 TTGTCGAATTTGATTTG
5448066 AGCATTGATG
Statistics
Matches: 66, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
30 7 0.11
31 59 0.89
ACGTcount: A:0.29, C:0.07, G:0.17, T:0.46
Consensus pattern (31 bp):
TTGTCGAATTTGATTTGTATATGGATATTCA
Found at i:5455360 original size:89 final size:89
Alignment explanation
Indices: 5455209--5455384 Score: 318
Period size: 89 Copynumber: 2.0 Consensus size: 89
5455199 GATGACATAG
*
5455209 TTGTGTTAGATTAATTACATTTTTTAACTTAGAATTATTAAACTCATGTTTATATTGTTACGAAT
1 TTGTGTTAGATTAATTACATTTCTTAACTTAGAATTATTAAACTCATGTTTATATTGTTACGAAT
*
5455274 AAGTTCACGGCAACTCGGTAATAA
66 AAGTTCACGACAACTCGGTAATAA
5455298 TTGTGTTCA-ATTAATTACATTTCTTAACTTAGAATTATTAAACTCATGTTTATATTGTTACGAA
1 TTGTGTT-AGATTAATTACATTTCTTAACTTAGAATTATTAAACTCATGTTTATATTGTTACGAA
5455362 TAAGTTCACGACAACTCGGTAAT
65 TAAGTTCACGACAACTCGGTAAT
5455385 TTGCTAACTT
Statistics
Matches: 84, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
89 83 0.99
90 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.41
Consensus pattern (89 bp):
TTGTGTTAGATTAATTACATTTCTTAACTTAGAATTATTAAACTCATGTTTATATTGTTACGAAT
AAGTTCACGACAACTCGGTAATAA
Found at i:5460454 original size:30 final size:28
Alignment explanation
Indices: 5460395--5460450 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
5460385 GATTTTTAAA
* *
5460395 AATATTTAAAAAAAGGCATCTAATATTT
1 AATATTTAAAAAAAGGCAACAAATATTT
*
5460423 AATATTTACAAAAAGAGCAACAAA-ATTT
1 AATATTTAAAAAAAG-GCAACAAATATTT
5460451 TTAAAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 18 0.75
29 6 0.25
ACGTcount: A:0.54, C:0.09, G:0.07, T:0.30
Consensus pattern (28 bp):
AATATTTAAAAAAAGGCAACAAATATTT
Found at i:5478516 original size:20 final size:22
Alignment explanation
Indices: 5478474--5478516 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
5478464 AGCTTGTGTT
* *
5478474 AATATGGTGTTTTTATGCTTAA
1 AATATGGTGTTTTTAAGCGTAA
5478496 AATA-GGTGTTTTTAAG-GTAA
1 AATATGGTGTTTTTAAGCGTAA
5478516 A
1 A
5478517 CAATAAGGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 11 0.58
22 4 0.21
ACGTcount: A:0.33, C:0.02, G:0.21, T:0.44
Consensus pattern (22 bp):
AATATGGTGTTTTTAAGCGTAA
Found at i:5478521 original size:22 final size:22
Alignment explanation
Indices: 5478474--5478521 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
5478464 AGCTTGTGTT
* *
5478474 AATATGGTGTTTTTATGCTTAA
1 AATATGGTGTTTTTAAGCTAAA
*
5478496 AATA-GGTGTTTTTAAGGTAAA
1 AATATGGTGTTTTTAAGCTAAA
5478517 CAATA
1 -AATA
5478522 AGGTATTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.35, C:0.04, G:0.19, T:0.42
Consensus pattern (22 bp):
AATATGGTGTTTTTAAGCTAAA
Found at i:5491111 original size:14 final size:14
Alignment explanation
Indices: 5491092--5491118 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5491082 GAGGTCCAGT
5491092 TGAACTGAACCGAG
1 TGAACTGAACCGAG
5491106 TGAACTGAACCGA
1 TGAACTGAACCGA
5491119 CCAAGAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.22, G:0.26, T:0.15
Consensus pattern (14 bp):
TGAACTGAACCGAG
Found at i:5495466 original size:16 final size:17
Alignment explanation
Indices: 5495431--5495464 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
5495421 CACATCTTTC
5495431 CTCTCTTCTCTCCATTTT
1 CTCTCTTCTCTCCA-TTT
*
5495449 CTCTCTTCTTTCCATT
1 CTCTCTTCTCTCCATT
5495465 CTAAAATTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 2 0.13
18 13 0.87
ACGTcount: A:0.06, C:0.38, G:0.00, T:0.56
Consensus pattern (17 bp):
CTCTCTTCTCTCCATTT
Found at i:5498227 original size:50 final size:50
Alignment explanation
Indices: 5498112--5498304 Score: 269
Period size: 50 Copynumber: 3.8 Consensus size: 50
5498102 GATAATAACA
* * * * ** *
5498112 TGCCAAAGTCATGTCCCAGACATGGTCTTACTTGAGATGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* **
5498163 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
5498213 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
5498263 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
5498305 TTACCAAAAT
Statistics
Matches: 127, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
50 96 0.76
51 31 0.24
ACGTcount: A:0.20, C:0.30, G:0.23, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:5506077 original size:22 final size:22
Alignment explanation
Indices: 5506052--5506097 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
5506042 CAAACCGAAA
* *
5506052 CACCACTATACAACCACCATAG
1 CACCACCACACAACCACCATAG
*
5506074 CACCACCACACCACCACCATAG
1 CACCACCACACAACCACCATAG
5506096 CA
1 CA
5506098 TAACCATATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.48, G:0.04, T:0.09
Consensus pattern (22 bp):
CACCACCACACAACCACCATAG
Found at i:5506078 original size:11 final size:11
Alignment explanation
Indices: 5506064--5506124 Score: 59
Period size: 11 Copynumber: 5.5 Consensus size: 11
5506054 CCACTATACA
5506064 ACCACCATAGC
1 ACCACCATAGC
* *
5506075 ACCACCACACC
1 ACCACCATAGC
5506086 ACCACCATAGC
1 ACCACCATAGC
** *
5506097 ATAACCATATC
1 ACCACCATAGC
* *
5506108 ACCACCCTTGC
1 ACCACCATAGC
5506119 ACCACC
1 ACCACC
5506125 TCCACAGCTG
Statistics
Matches: 38, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
11 38 1.00
ACGTcount: A:0.34, C:0.49, G:0.05, T:0.11
Consensus pattern (11 bp):
ACCACCATAGC
Done.